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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:20, 17 September 2013


Full id: C326_bile_choriocarcinoma_giant_lung_mucinous_glassy_malignant



Phase1 CAGE Peaks

Hg19::chr10:128112935..128112946,+p@chr10:128112935..128112946
+
Hg19::chr10:5075825..5075836,+p@chr10:5075825..5075836
+
Hg19::chr10:5075837..5075848,+p@chr10:5075837..5075848
+
Hg19::chr11:110129024..110129031,-p19@RDX
Hg19::chr11:110129088..110129096,-p18@RDX
Hg19::chr11:41899631..41899640,-p@chr11:41899631..41899640
-
Hg19::chr12:132340327..132340336,+p@chr12:132340327..132340336
+
Hg19::chr12:15815672..15815681,-p27@EPS8
Hg19::chr12:15815704..15815714,-p24@EPS8
Hg19::chr12:19842219..19842224,+p@chr12:19842219..19842224
+
Hg19::chr12:19842253..19842299,+p@chr12:19842253..19842299
+
Hg19::chr12:19842421..19842428,+p@chr12:19842421..19842428
+
Hg19::chr12:19842430..19842437,+p@chr12:19842430..19842437
+
Hg19::chr12:19842439..19842446,+p@chr12:19842439..19842446
+
Hg19::chr14:32476072..32476090,+p1@ENST00000556949
Hg19::chr15:75682218..75682225,-p@chr15:75682218..75682225
-
Hg19::chr15:75682252..75682263,-p@chr15:75682252..75682263
-
Hg19::chr15:89659033..89659044,+p@chr15:89659033..89659044
+
Hg19::chr17:77809975..77809980,-p@chr17:77809975..77809980
-
Hg19::chr19:16023475..16023478,-p@chr19:16023475..16023478
-
Hg19::chr1:164600166..164600175,+p47@PBX1
Hg19::chr1:164600184..164600191,+p38@PBX1
Hg19::chr1:197964894..197964906,-p@chr1:197964894..197964906
-
Hg19::chr1:241804444..241804477,-p@chr1:241804444..241804477
-
Hg19::chr2:239198771..239198784,-p7@PER2
Hg19::chr3:192362159..192362169,-p@chr3:192362159..192362169
-
Hg19::chr4:178243549..178243558,+p@chr4:178243549..178243558
+
Hg19::chr5:66178685..66178698,+p@chr5:66178685..66178698
+
Hg19::chr5:66178707..66178713,+p@chr5:66178707..66178713
+
Hg19::chr6:79960170..79960171,-p@chr6:79960170..79960171
-
Hg19::chr7:128543063..128543091,-p@chr7:128543063..128543091
-
Hg19::chr7:143953304..143953314,-p1@uc003wed.2
Hg19::chr7:143953331..143953349,-p1@OR2A20P
Hg19::chr7:389967..389980,+p@chr7:389967..389980
+
Hg19::chr9:131397542..131397587,-p@chr9:131397542..131397587
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0030033microvillus biogenesis0.0173045506176316
GO:0032528microvillus organization and biogenesis0.0173045506176316
GO:0051123transcriptional preinitiation complex assembly0.0173045506176316
GO:0045898regulation of transcriptional preinitiation complex assembly0.0173045506176316
GO:0032420stereocilium0.0173045506176316
GO:0032421stereocilium bundle0.0173045506176316
GO:0045176apical protein localization0.0188726906492033
GO:0030175filopodium0.0188726906492033
GO:0008105asymmetric protein localization0.0188726906492033
GO:0007016cytoskeletal anchoring0.0188726906492033
GO:0006700C21-steroid hormone biosynthetic process0.0188726906492033
GO:0008207C21-steroid hormone metabolic process0.0198852996184453
GO:0005902microvillus0.0198852996184453
GO:0051693actin filament capping0.0198852996184453
GO:0007530sex determination0.0198852996184453
GO:0051016barbed-end actin filament capping0.0198852996184453
GO:0030835negative regulation of actin filament depolymerization0.0198852996184453
GO:0030902hindbrain development0.0198852996184453
GO:0030834regulation of actin filament depolymerization0.0198852996184453
GO:0030042actin filament depolymerization0.0198852996184453
GO:0007623circadian rhythm0.023872501376074
GO:0007173epidermal growth factor receptor signaling pathway0.0259258954015117
GO:0030027lamellipodium0.0261884710132444
GO:0005515protein binding0.0261884710132444
GO:0042446hormone biosynthetic process0.0261884710132444
GO:0001726ruffle0.0261884710132444
GO:0008064regulation of actin polymerization and/or depolymerization0.0261884710132444
GO:0051261protein depolymerization0.0261884710132444
GO:0030832regulation of actin filament length0.0261884710132444
GO:0032535regulation of cellular component size0.0261884710132444
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0261884710132444
GO:0005070SH3/SH2 adaptor activity0.0264473229556302
GO:0051129negative regulation of cellular component organization and biogenesis0.0270318444045401
GO:0051493regulation of cytoskeleton organization and biogenesis0.0270318444045401
GO:0033043regulation of organelle organization and biogenesis0.0270318444045401
GO:0019222regulation of metabolic process0.0270318444045401
GO:0060090molecular adaptor activity0.0277109664806096
GO:0008154actin polymerization and/or depolymerization0.0277109664806096
GO:0031252leading edge0.0318538779589705
GO:0045177apical part of cell0.0356548518296873
GO:0003006reproductive developmental process0.0356548518296873
GO:0042445hormone metabolic process0.0356548518296873
GO:0006694steroid biosynthetic process0.0356548518296873
GO:0030674protein binding, bridging0.0356548518296873
GO:0051128regulation of cellular component organization and biogenesis0.0382952347115228
GO:0051248negative regulation of protein metabolic process0.0389543544901542
GO:0019898extrinsic to membrane0.0392201151579407
GO:0050954sensory perception of mechanical stimulus0.0463576165769469
GO:0007605sensory perception of sound0.0463576165769469
GO:0007420brain development0.0476834017488412
GO:0050794regulation of cellular process0.0476834017488412



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
bile duct7.67e-186
digestive system duct7.67e-186
biliary system2.19e-129
biliary tree2.19e-129
biliary bud2.19e-129
Disease
Ontology termp-valuen
lung cancer5.93e-0815
respiratory system cancer1.54e-0716


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.18.04491e-07
MA0004.10.0714537
MA0006.11.05493
MA0007.10.0639049
MA0009.11.70901
MA0014.12.23795e-05
MA0017.10.125199
MA0019.10.145319
MA0024.10.285711
MA0025.12.08402
MA0027.11.89328
MA0028.10.258143
MA0029.10.30014
MA0030.10.79265
MA0031.11.96692
MA0038.10.382097
MA0040.10.304553
MA0041.10.574136
MA0042.10.065999
MA0043.10.366755
MA0046.11.67881
MA0048.10.0347795
MA0050.10.066352
MA0051.10.118004
MA0052.10.307481
MA0055.10.070867
MA0056.10
MA0057.10.00249228
MA0058.10.0375298
MA0059.10.146942
MA0060.10.0266319
MA0061.10.0571069
MA0063.10
MA0066.10.382686
MA0067.10.638784
MA0068.10.0315947
MA0069.10.354782
MA0070.10.345954
MA0071.10.675927
MA0072.10.906843
MA0073.11.53748e-05
MA0074.10.117607
MA0076.10.665178
MA0077.10.336397
MA0078.10.175262
MA0081.10.340864
MA0083.10.372513
MA0084.10.811454
MA0087.10.902582
MA0088.10.0432759
MA0089.10
MA0090.10.400602
MA0091.10.918907
MA0092.10.209949
MA0093.10.0954868
MA0095.10
MA0098.10
MA0100.11.30016
MA0101.10.0226238
MA0103.11.39112
MA0105.10.00170028
MA0106.10.440452
MA0107.10.00986632
MA0108.21.26212
MA0109.10
MA0111.10.192269
MA0113.10.152632
MA0114.10.0468005
MA0115.10.570409
MA0116.10.0513915
MA0117.10.396851
MA0119.10.311459
MA0122.10.418111
MA0124.10.533912
MA0125.13.0178
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.10.391883
MA0139.10.366721
MA0140.10.0991227
MA0141.10.145306
MA0142.10.633705
MA0143.10.906802
MA0144.10.932046
MA0145.10.107375
MA0146.10.00149708
MA0147.10.294751
MA0148.12.64643
MA0149.10.0944562
MA0062.20.124078
MA0035.20.0987789
MA0039.20.00051361
MA0138.20.176028
MA0002.20.699203
MA0137.20.50116
MA0104.20.176968
MA0047.24.1636
MA0112.20.0222903
MA0065.20.0111203
MA0150.13.17187
MA0151.10
MA0152.10.684929
MA0153.11.98554
MA0154.10.00704234
MA0155.10.00192196
MA0156.10.272778
MA0157.11.74969
MA0158.10
MA0159.10.29618
MA0160.10.299258
MA0161.10
MA0162.10.000147124
MA0163.10.000458977
MA0164.10.160035
MA0080.20.0219279
MA0018.20.143876
MA0099.22.93751
MA0079.21.44649e-15
MA0102.20.846442
MA0258.10.218761
MA0259.10.80596
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#1051153.416206125353498.07454372054656e-060.000224281189263341
EP300#2033142.709576690489280.0002469507419952580.00268491448503464
FOS#2353112.827928811366810.001038395056170170.00734350902433348
JUN#3725134.647622271439211.47511420509808e-065.69325397140569e-05
JUND#3727142.797865576748410.0001748265937413490.00212681591424027
NR3C1#2908104.278006666049446.83167969732869e-050.00109030225536264
POLR3A#11128219.37897771952820.00484166966546120.0226915786300082
STAT3#6774123.606673713310035.5685080397802e-050.000940746378464257



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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